MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000377893
MT speed 0 s - this script 3.161107 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GPR153	polymorphism_automatic	0.589357600801755	simple_aae		affected		R209H	single base exchange	rs12735670		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.410642399198245 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:6313938C>TN/A show variant in all transcripts IGV

HGNC symbol

GPR153

Ensembl transcript ID

ENST00000377893

Genbank transcript ID

NM_207370

UniProt peptide

Q6NV75

alteration type

single base exchange

alteration region

CDS

DNA changes

c.626G>A
cDNA.886G>A
g.7098G>A

AA changes

R209H Score: 29 explain score(s)

position(s) of altered AA
if AA alteration in CDS

209

frameshift

known variant

Reference ID: rs12735670

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1250	1001	2251
ExAC	27309	-21851	5458

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.951	0.956
	0.979	0.988
(flanking)	3.139	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	7090	wt: 0.31 / mu: 0.68	wt: CGCCAGGCCGACCGC mu: CGCCAGGCCGACCAC	CCAG\|gccg

distance from splice site

161

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

209

mutated

not conserved

209

Ptroglodytes

all identical

ENSPTRG00000000082

209

Mmulatta

all identical

ENSMMUG00000004092

209

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000042804

209

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000015145

208

Drerio

no alignment

ENSDARG00000087601

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000001154

209

protein features

start (aa)	end (aa)	feature	details
197	243	TOPO_DOM	Cytoplasmic (Potential).	lost
244	264	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
265	276	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
277	297	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
298	609	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
479	552	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
579	582	COMPBIAS	Poly-Gly.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1830 / 1830

position (AA) of stopcodon in wt / mu AA sequence

610 / 610

position of stopcodon in wt / mu cDNA

2090 / 2090

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

261 / 261

chromosome

strand

-1

last intron/exon boundary

1425

theoretical NMD boundary in CDS

1114

length of CDS

1830

coding sequence (CDS) position

626

cDNA position
(for ins/del: last normal base / first normal base)

886

gDNA position
(for ins/del: last normal base / first normal base)

7098

chromosomal position
(for ins/del: last normal base / first normal base)

6313938

original gDNA sequence snippet

GGTGGGGCGCCAGGCCGACCGCCGCGCCTTCACCGTGCCCA

altered gDNA sequence snippet

GGTGGGGCGCCAGGCCGACCACCGCGCCTTCACCGTGCCCA

original cDNA sequence snippet

GGTGGGGCGCCAGGCCGACCGCCGCGCCTTCACCGTGCCCA

altered cDNA sequence snippet

GGTGGGGCGCCAGGCCGACCACCGCGCCTTCACCGTGCCCA

wildtype AA sequence

MSDERRLPGS AVGWLVCGGL SLLANAWGIL SVGAKQKKWK PLEFLLCTLA ATHMLNVAVP
IATYSVVQLR RQRPDFEWNE GLCKVFVSTF YTLTLATCFS VTSLSYHRMW MVCWPVNYRL
SNAKKQAVHT VMGIWMVSFI LSALPAVGWH DTSERFYTHG CRFIVAEIGL GFGVCFLLLV
GGSVAMGVIC TAIALFQTLA VQVGRQADRR AFTVPTIVVE DAQGKRRSSI DGSEPAKTSL
QTTGLVTTIV FIYDCLMGFP VLVVSFSSLR ADASAPWMAL CVLWCSVAQA LLLPVFLWAC
DRYRADLKAV REKCMALMAN DEESDDETSL EGGISPDLVL ERSLDYGYGG DFVALDRMAK
YEISALEGGL PQLYPLRPLQ EDKMQYLQVP PTRRFSHDDA DVWAAVPLPA FLPRWGSGED
LAALAHLVLP AGPERRRASL LAFAEDAPPS RARRRSAESL LSLRPSALDS GPRGARDSPP
GSPRRRPGPG PRSASASLLP DAFALTAFEC EPQALRRPPG PFPAAPAAPD GADPGEAPTP
PSSAQRSPGP RPSAHSHAGS LRPGLSASWG EPGGLRAAGG GGSTSSFLSS PSESSGYATL
HSDSLGSAS*

mutated AA sequence

MSDERRLPGS AVGWLVCGGL SLLANAWGIL SVGAKQKKWK PLEFLLCTLA ATHMLNVAVP
IATYSVVQLR RQRPDFEWNE GLCKVFVSTF YTLTLATCFS VTSLSYHRMW MVCWPVNYRL
SNAKKQAVHT VMGIWMVSFI LSALPAVGWH DTSERFYTHG CRFIVAEIGL GFGVCFLLLV
GGSVAMGVIC TAIALFQTLA VQVGRQADHR AFTVPTIVVE DAQGKRRSSI DGSEPAKTSL
QTTGLVTTIV FIYDCLMGFP VLVVSFSSLR ADASAPWMAL CVLWCSVAQA LLLPVFLWAC
DRYRADLKAV REKCMALMAN DEESDDETSL EGGISPDLVL ERSLDYGYGG DFVALDRMAK
YEISALEGGL PQLYPLRPLQ EDKMQYLQVP PTRRFSHDDA DVWAAVPLPA FLPRWGSGED
LAALAHLVLP AGPERRRASL LAFAEDAPPS RARRRSAESL LSLRPSALDS GPRGARDSPP
GSPRRRPGPG PRSASASLLP DAFALTAFEC EPQALRRPPG PFPAAPAAPD GADPGEAPTP
PSSAQRSPGP RPSAHSHAGS LRPGLSASWG EPGGLRAAGG GGSTSSFLSS PSESSGYATL
HSDSLGSAS*

speed

0.90 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems